SeqAn3  3.0.3
The Modern C++ library for sequence analysis.
seqan3::rna5 Class Reference

The five letter RNA alphabet of A,C,G,U and the unknown character N. More...

#include <seqan3/alphabet/nucleotide/rna5.hpp>

+ Inheritance diagram for seqan3::rna5:

Public Member Functions

Constructors, destructor and assignment
constexpr rna5 () noexcept=default
 Defaulted.
 
constexpr rna5 (rna5 const &) noexcept=default
 Defaulted.
 
constexpr rna5 (rna5 &&) noexcept=default
 Defaulted.
 
constexpr rna5operator= (rna5 const &) noexcept=default
 Defaulted.
 
constexpr rna5operator= (rna5 &&) noexcept=default
 Defaulted.
 
 ~rna5 () noexcept=default
 Defaulted.
 
constexpr rna5 (dna5 const &r) noexcept
 Allow implicit construction from dna/rna of the same size. More...
 
- Public Member Functions inherited from seqan3::nucleotide_base< rna5, 5 >
constexpr nucleotide_base (other_nucl_type const &other) noexcept
 Allow explicit construction from any other nucleotide type and convert via the character representation. More...
 
constexpr rna5 complement () const noexcept
 Return the complement of the letter. More...
 
- Public Member Functions inherited from seqan3::alphabet_base< derived_type, size, char_t >
constexpr alphabet_base () noexcept=default
 Defaulted.
 
constexpr alphabet_base (alphabet_base const &) noexcept=default
 Defaulted.
 
constexpr alphabet_base (alphabet_base &&) noexcept=default
 Defaulted.
 
constexpr alphabet_baseoperator= (alphabet_base const &) noexcept=default
 Defaulted.
 
constexpr alphabet_baseoperator= (alphabet_base &&) noexcept=default
 Defaulted.
 
 ~alphabet_base () noexcept=default
 Defaulted.
 
constexpr char_type to_char () const noexcept
 Return the letter as a character of char_type. More...
 
constexpr rank_type to_rank () const noexcept
 Return the letter's numeric value (rank in the alphabet). More...
 
constexpr derived_type & assign_char (char_type const chr) noexcept
 Assign from a character, implicitly converts invalid characters. More...
 
constexpr derived_type & assign_rank (rank_type const c) noexcept
 Assign from a numeric value. More...
 

Related Functions

(Note that these are not member functions.)

using rna5_vector = std::vector< rna5 >
 Alias for an std::vector of seqan3::rna5. More...
 
Nucleotide literals
constexpr rna5 operator""_rna5 (char const c) noexcept
 The seqan3::rna5 char literal. More...
 
rna5_vector operator""_rna5 (char const *s, std::size_t n)
 The seqan3::rna5 string literal. More...
 

Additional Inherited Members

- Static Public Member Functions inherited from seqan3::nucleotide_base< rna5, 5 >
static constexpr bool char_is_valid (char_type const c) noexcept
 Validate whether a character value has a one-to-one mapping to an alphabet value. More...
 
- Static Public Attributes inherited from seqan3::alphabet_base< derived_type, size, char_t >
static constexpr detail::min_viable_uint_t< size > alphabet_size = size
 The size of the alphabet, i.e. the number of different values it can take. More...
 
- Protected Types inherited from seqan3::alphabet_base< derived_type, size, char_t >
using char_type = std::conditional_t< std::same_as< char_t, void >, char, char_t >
 The char representation; conditional needed to make semi alphabet definitions legal. More...
 
using rank_type = detail::min_viable_uint_t< size - 1 >
 The type of the alphabet when represented as a number (e.g. via to_rank()). More...
 

Detailed Description

The five letter RNA alphabet of A,C,G,U and the unknown character N.

This alphabet has the same internal representation as seqan3::dna5, the only difference is that it prints 'U' on character conversion instead of 'T'. You can assign between values of seqan3::dna5 and seqan3::rna5.

Like most alphabets, this alphabet cannot be initialised directly from its character representation. Instead initialise/assign from the character literal or use the function seqan3::rna5::assign_char().

int main()
{
using namespace seqan3::literals;
seqan3::rna5 letter{'A'_rna5};
letter.assign_char('C');
seqan3::debug_stream << letter << '\n'; // prints "C"
letter.assign_char('F'); // Unknown characters are implicitly converted to N.
seqan3::debug_stream << letter << '\n'; // prints "N"
}
constexpr derived_type & assign_char(char_type const chr) noexcept
Assign from a character, implicitly converts invalid characters.
Definition: alphabet_base.hpp:211
The five letter RNA alphabet of A,C,G,U and the unknown character N.
Definition: rna5.hpp:49
Provides seqan3::debug_stream and related types.
debug_stream_type debug_stream
A global instance of seqan3::debug_stream_type.
Definition: debug_stream.hpp:42
The SeqAn namespace for literals.
Provides seqan3::rna5, container aliases and string literals.

This entity is stable. Since version 3.1.

Constructor & Destructor Documentation

◆ rna5()

constexpr seqan3::rna5::rna5 ( dna5 const &  r)
inlineconstexprnoexcept

Allow implicit construction from dna/rna of the same size.

This entity is stable. Since version 3.1.

Friends And Related Function Documentation

◆ operator""_rna5() [1/2]

rna5_vector operator""_rna5 ( char const *  s,
std::size_t  n 
)
related

The seqan3::rna5 string literal.

Returns
seqan3::rna5_vector

You can use this string literal to easily assign to rna5_vector:

int main()
{
using namespace seqan3::literals;
seqan3::rna5_vector sequence1{"ACGTTA"_rna5};
seqan3::rna5_vector sequence2 = "ACGTTA"_rna5;
auto sequence3 = "ACGTTA"_rna5;
}

This entity is stable. Since version 3.1.

◆ operator""_rna5() [2/2]

constexpr rna5 operator""_rna5 ( char const  c)
related

The seqan3::rna5 char literal.

Returns
seqan3::rna5

You can use this char literal to assign a seqan3::rna5 character:

int main()
{
using namespace seqan3::literals;
seqan3::rna5 letter1{'A'_rna5};
auto letter2 = 'A'_rna5;
}

This entity is stable. Since version 3.1.

◆ rna5_vector

using rna5_vector = std::vector<rna5>
related

Alias for an std::vector of seqan3::rna5.

This entity is stable. Since version 3.1.


The documentation for this class was generated from the following file: